2018

Miladys Limonta, Lourdes Zumalacarregui, Urska Vidic, Nika Lendero Krajnc

The main component of the Center for Genetic Engineering and Biotechnology (CIGB) candidate vaccine against Hepatitis C virus (HCV) is the pIDKE2 plasmid. The current designed downstream process for the production of pIDKE2 fulfils all regulatory requirements and renders the required quantities of pharamceutical-grade plasmid DNA (pDNA)with 95% purity. The advantages of this procedure include high plasmid purity and the elimination of undesirable additives. such as toxic organic extractants and animal-derived enzymes. However, yields and consequently the productivity of the process are low. Previous work demonstrated that the most critical step of the process is the reverse phase chromatography, where conventional porous particle resins are used. Therefore, to increase the process productivity alternative technologies such as membranes and chromatographic monoliths were tested as alternative options for this critical step. Here, a comparison between the behaviours of CIM® C4-HLD and Sartobind phenyl matrices was performed.

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Tsutomu Arakawa, Pete Gagnon

Journal of Pharmaceutical Sciences 107 (2018) 2297-2305

The concept of cosolvent exclusion was developed by a group of Timasheff's laboratory in 1970-1990 and is currently used widely to explain the effects of a variety of cosolvents on the stability and solubility of macromolecules. Not surprisingly, these concepts have had substantial influence in the fields of formulation, protein folding and unfolding, but they have perhaps more surprisingly found their way into the field of chromatography. A variety of excluded cosolvents have been used to enhance binding and resolution of proteins and other macromolecules in ion exchange, hydroxyapatite, affinity, and hydrophobic interaction chromatography. These cosolvents include salting-out salts, amino acids and polymers, and frequently polyethylene glycol (PEG). A new mode of chromatography, termed “steric exclusion chromatography,” was recently introduced. It employs hydroxylated solid phase surfaces. Steric exclusion of the PEG stabilizes the association of macromolecules with the solid phase. Elution is achieved by reducing the PEG concentration. Magnetic particles are also used in this chromatography. This review summarizes the concepts of preferential cosolvent exclusion and its applications in column chromatography.

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2017

V.Rajamanickam, D.Wurm, C.Slouka, C.Herwig, O.Spadiut

Anal Bioanal Chem (2016)

The bacterium Escherichia coli is a well-studied recombinant host organism with a plethora of applications in biotechnology. Highly valuable biopharmaceuticals, such as antibody fragments and growth factors, are currently being produced in E. coli. However, the high metabolic burden during recombinant protein production can lead to cell death, consequent lysis, and undesired product loss. Thus, fast and precise analyzers to monitor E. coli bioprocesses and to retrieve key process information, such as the optimal time point of harvest, are needed. However, such reliable monitoring tools are still scarce to date. In this study, we cultivated an E. coli strain producing a recombinant single-chain antibody fragment in the cytoplasm. In bioreactor cultivations, we purposely triggered cell lysis by pH ramps. We developed a novel toolbox using UV chromatograms as fingerprints and chemometric techniques to monitor these lysis events and used flow cytometry (FCM) as reference method to quantify viability offline. Summarizing, we were able to show that a novel toolbox comprising HPLC chromatogram fingerprinting and data science tools allowed the identification of E. coli lysis in a fast and reliable manner. We are convinced that this toolbox will not only facilitate E. coli bioprocess monitoring but will also allow enhanced process control in the future

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Sebastijan Peljhan, Tina Jakop, Dunja Šček, Vid Skvarča, Blaž Goričar, Romina Žabar, Nina Mencin. Electrophoresis 2017 July 20

The plasma-derived IgG used either for diagnostic purpose or intravenous application (in form of IVIG) in various medical therapies is certainly gaining more and more attention on annual basis. Different manufacturing processes are used to isolate immunoglobulins from human plasma. However, a quest for alternative paths in IgG isolation not only requires development of the most efficient isolation process, but also a rapid and reliable analytics to track the purification. Fast and reliable fingerprint based method for characterization of IgG prepared from Cohn I+II+III paste is presented in this paper. The fingerprint method bases on partial separation of proteins in linear gradient on CIMacTM quaternary amine, strong anion exchange group (QA) 0.1 mL column. Partial separation of proteins does not allow simple quantitative analysis of the samples during the IgG isolation from Cohn I+II+III fraction paste, but very accurate qualitative information about the composition of the sample can be obtained in less than 5 min. From the differences in the chromatograms of various samples, the ratio between IgG and impurities in each sample can be easily assessed. The method is suitable for input material control, in-line monitoring of the downstream processing, final control of the products, as well as in stability studies and enables taking fast and accurate decisions during fractionation process.

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Antonio M. Munoz, Paul Yourik, Vaishnavi Rajagopal, Jagpreet S. Nanda, Jon R. Lorsch, Sarah E. Walker

RNA Biology, 2017, VOL. 14, NO. 2, 188–196

In vitro studies of translation provide critical mechanistic details, yet purification of large amounts of highly active eukaryotic ribosomes remains a challenge for biochemists and structural biologists. Here, we present an optimized method for preparation of highly active yeast ribosomes that could easily be adapted for purification of ribosomes from other species. The use of a nitrogen mill for cell lysis coupled with chromatographic purification of the ribosomes results in 10-fold-increased yield and less variability compared with the traditional approach, which relies on sedimentation through sucrose cushions. We demonstrate that these ribosomes are equivalent to those made using the traditional method in a host of in vitro assays, and that utilization of this new method will consistently produce high yields of active yeast ribosomes.

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2015

A.M. Almeida, J.A. Queiroz, F. Sousa, A. Sousa

Journal of Chromatography B, 978–979 (2015) 145–150

The progress of DNA vaccines is dependent on the development of suitable chromatographic procedures to successfully purify genetic vectors, such as plasmid DNA. Human Papillomavirus is associated with the development of tumours due to the oncogenic power of E6 and E7 proteins, produced by this virus. The supercoiled HPV-16 E6/E7 plasmid-based vaccine was recently purified with the arginine monolith, with 100% of purity, but only 39% of recovery was achieved. Therefore, the present study describes the application of experimental design tools, a newly explored methodology in preparative chromatography, in order to improve the supercoiled plasmid DNA recovery with the arginine monolith, maintaining the high purity degree. In addition, the importance and influence of pH in the pDNA retention to the arginine ligand was also demonstrated. The Composite Central Face design was validated and the recovery of the target molecule was successfully improved from 39% to 83.5%, with an outstanding increase of more than double, while maintaining 100% of purity.

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D. Buzzi, A. Štrancar

Chimica Oggi-Chemistry Today; Vol 33(1) January/February 2015

The importance of the monitoring of a process all along its steps by means of PAT has been defined by FDA in 2002. How can be defined the product quality and what are the parameters that should be checked by means of different analysis techniques, being focused in particular on the application of high pressure liquid chromatography techniques (HPLC) as high value tool for the process monitoring. From the first introduction of Process Analytical Technology to the "state of the art": how can be PAT implemented in order to ensure the final product quality.

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Zunyang Ke, Yu Wang and Zhongming Li

Anion-exchange chromatography is a key capture step in downstream processing plasmid DNA (pDNA). Separation of pDNA using traditional particle-based anion-exchange supports is usually slow and has a low capacity for pDNA due to steric exclusion effects. Due to convective mass transfer properties, and large flow-through channels for binding large biomolecules, monoliths have been shown to provide a fast and efficient alternative for pDNA purification. This study describes the use of monoliths for purification of a therapeutic pDNA vaccine against multidrug resistant tuberculosis (MDR TB).

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P. Kramberger, U. Lidija, A. Štrancar
Human Vaccines & Immunotherapeutics, 11:4 (2015) 1010-1021

Downstream processing of nanoplexes (viruses, virus-like particles, bacteriophages) is characterized by complexity of the starting material, number of purification methods to choose from, regulations that are setting the frame for the final product and analytical methods for upstream and downstream monitoring. This review gives an overview on the nanoplex downstream challenges and chromatography based analytical methods for efficient monitoring of the nanoplex production.

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A. G. Lopes

FBP-461, Food and Bioproducts Processing (2014)

As the biopharmaceutical industry matures, the trend towards increased flexibility and productivity, faster time tomarket and greater profitability are driving the replacement of traditional stainless steel equipment by single-use technology (SUT). The use of SUT in the biopharmaceutical industry can significantly impact the manufacturing process efficiency by reducing capital costs, improving plant flexibility, reducing start-up times and costs, and elim-inating both non-value added process steps and the risk of cross-contamination. In addition it significantly reduces process liquid waste, labour costs and on-site quality and validation requirements. This paper reviews the current status of the technology and the impact of SUT in the biopharmaceutical industry, with the aim of identifying the challenges and limitations that still need to be addressed for further adoption of these technologies. Even tough SUT has a multitude of systems available, its components and assemblies have little standardisation as well as alack of harmonised tests and procedures among suppliers, with an array of guidelines from a variety of sourcesand no critical limits have been established. In addition, the use of SUT has new validation requirements such as leachables and extractables, suppliers’ qualification and SUT lot-to-lot variability. The lack of expertise in these areas and the new training requirements when using SUT also need to be addressed. To date the majority of the avail-able literature regarding SUT is found in trade journals where typically suppliers are the main contributors. There is still a lack of engagement of the academic community, which contributes to very limited scientific proof from independent peer-reviewed research to support performance of SUT. This is particularly the case during operation and integrity testing of SUT, during for example on-site testing, transport and disposal. Another area where no work has been undertaken concerns conceptual approaches for facility clean-room requirement and appropriate layout design using SUT. Investment in novel technologies, research, standardisation and training is paramount for further development and implementation of SUTs across all sectors of the biopharmaceutical industry.

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Urh Černigoj, Urška Martinuč, Sara Cardoso, Rok Sekirnik, Nika Lendero Krajnc, Aleš Štrancar

Sample displacement chromatography (SDC) is a chromatographic technique that utilises different rela-tive binding affinities of components in a sample mixture and has been widely studied in the context ofpeptide and protein purification. Here, we report a use of SDC to separate plasmid DNA (pDNA) isoformsunder overloading conditions, where supercoiled (sc) isoform acts as a displacer of open circular (oc) orlinear isoform. Since displacement is more efficient when mass transfer between stationary and mobilechromatographic phases is not limited by diffusion, we investigated convective interaction media (CIM)monoliths as stationary phases for pDNA isoform separation. CIM monoliths with different hydrophobic-ities and thus different binding affinities for pDNA (CIM C4 HLD, CIM-histamine and CIM-pyridine) weretested under hydrophobic interaction chromatography (HIC) conditions. SD efficiency for pDNA isoformseparation was shown to be dependent on column selectivity for individual isoform, column efficiencyand on ammonium sulfate (AS) concentration in loading buffer (binding strength). SD and negative modeelution often operate in parallel, therefore negative mode elution additionally influences the efficiencyof the overall purification process. Optimisation of chromatographic conditions achieved 98% sc pDNAhomogeneity and a dynamic binding capacity of over 1 mg/mL at a relatively low concentration of AS.SDC was successfully implemented for the enrichment of sc pDNA for plasmid vectors of different sizes,and for separation of linear and and sc isoforms, independently of oc:sc isoform ratio, and flow-rate used.This study therefore identifies SDC as a promising new approach to large-scale pDNA purification, whichis compatible with continuous, multicolumn chromatography systems, and could therefore be used toincrease productivity of pDNA production in the future.

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2013

A. A. Shukla, U. Gottschalk

Trends in Biotechnology (2012) 1-8

The manufacture of protein biopharmaceuticals is conducted under current good manufacturing practice (cGMP) and involves multiple unit operations for upstream production and downstream purification. Until recently, production facilities relied on the use of relatively inflexible, hard-piped equipment including large stainless steel bioreactors and tanks to hold product intermediates and buffers. However, there is an increasing trend towards the adoption of single-use technologies across the manufacturing process. Technical advances have now made an end-to-end single-use manufacturing facility possible, but several aspects of single-use technology require further improvement and are continually evolving. This article provides a perspective on the current state-of-the-art in single-use technologies and highlights trends that will improve performance and increase the market penetration of disposable manufacturing in the future.

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M. Li, Y. X. Qiu

Vaccine 31 (2013) 1264-1267

An effective downstream bio-processing of vaccine products requires complete chemical knowledge of the contaminants that may arise from a given vector expression system. Whether the vaccine is made from the traditional egg-based or the new cell-cultured process, it is the expression system that determines the types of impurities that need to be identified and removed from the vaccine product.

There are mechanical and chemical factors that can either reduce the yield or render a vaccine product to be irreversibly inactive. The choice of equipment and solvents is therefore important in minimizing product loss, and for maintaining an efficient and optimized manufacturing process.

The frequent out-of-specification, irreproducible data and inefficiency in the manufacturing of biologics were the basis for FDA to propose the “cGMP for the 21st Century” initiative in the year of 2000. Effective 2004, the concept of quality by design (QbD) has been imposed in the manufacturing of biologics. To facilitate the implementation of QbD FDA has encouraged the use of process analytical technology (PAT). Further, FDA believes that an optimized manufacturing scheme requires one to identify and to control the variables that can negatively affect the yield and quality of the desired product, and PAT can reveal wrongful data and alert the operator for immediate correction during processing.

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E. Mota, A. Sousa, U. Černigoj, J. A. Queiroz, C. T. Tomaz, F. Sousa

Journal of Chromatography A (2013)

The demand for high-purity supercoiled plasmid DNA to be applied as a vector for new therapeutic strategies, such as gene therapy or DNA vaccination has increased in the last years. Thus, it is necessary to implement an analytical technique suitable to control the quality of the supercoiled plasmid as a pharmaceutical product during the manufacturing process. The present study describes a new methodology to quantify and monitor the purity of supercoiled plasmid DNA by using a monolithic column based on anion-exchange chromatography. This analytical method with UV detection allows the separation of the plasmid isoforms by combining a NaCl stepwise gradient. The specificity, linearity, accuracy, reproducibility and repeatability of the method have been evaluated, and the lower quantification and detection limits were also established. The validation was performed according to the guidelines, being demonstrated that the method is precise and accurate for a supercoiled plasmid concentration up to 200 μg/mL. The main advantage achieved by using this monolithic column is the possibility to quantify the supercoiled plasmid in a sample containing other plasmid topologies, in a 4 min experiment. This column also permits the assessment of the supercoiled plasmid DNA present in more complex samples, allowing to control its quality throughout the bioprocess. Therefore, these findings strengthen the possibility of using this monolithic column associated with a powerful analytical method to control the process development of supercoiled plasmid DNA production and purification for therapeutic applications.

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S. Haberl, M. Jarc, A. Štrancar, M. Peterka, D. Hodžić, D. Miklavčič

J Membrane Biol, DOI 10.1007/s00232-013-9580-5

The use of plasmid DNA (pDNA) as a pharmaceutical tool has increased since it represents a safer vector for gene transfer compared to viral vectors. Different pDNA extraction methods have been described; among them is alkaline lysis, currently the most commonly used. Although alkaline lysis represents an established method for isolation of pDNA, some drawbacks are recognized, such as entrapment of pDNA in cell debris, leading to lower pDNA recovery; the time-consuming process; and increase of the volume due to the buffers used, all leading to increased cost of production. We compared the concentration of extracted pDNA when two methods for extracting pDNA from Escherichia coli were used: alkaline lysis and a method based on membrane electroporation, electroextraction. At the same time, we also studied the effect of different pulse protocols on bacterial inactivation. The concentration of pDNA was assayed with anion exchange chromatography. When alkaline lysis was used, two incubations of lysis time (5 and 10 min) were compared in terms of the amount of isolated pDNA. We did not observe any difference in pDNA concentration regardless of incubation time used. In electroextraction, different pulse protocols were used in order to exceed the pDNA concentration obtained by alkaline lysis. We show that electroextraction gives a higher concentration of extracted pDNA than alkaline lysis, suggesting the use of electroporation as a potentially superior method for extracting pDNA from E. coli. In addition, electroextraction represents a quicker alternative to alkaline lysis for extracting pDNA.

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B. Gabor, U. Černigoj, M. Barut, A. Štrancar

Journal of Chromatography A, 1311 (2013) 106-114

HPLC based analytical assay is a powerful technique that can be used to efficiently monitor plasmid DNA (pDNA) purity and quantity throughout the entire purification process. Anion exchange monolithic and non-porous particle based stationary phases were used to study the recovery of the different pDNA isoforms from the analytical column. Three differently sized pDNA molecules of 3.0 kbp, 5.2 kbp and 14.0 kbp were used. Plasmid DNA was injected onto columns under the binding conditions and the separation of the isoforms took place by increasing the ionic strength of the elution buffer. While there was no substantial decrease of the recovered supercoiled and linear isoforms of the pDNA with the increase of the plasmid size and with the increase of the flow rate (recoveries in all cases larger than 75%), a pronounced decrease of the oc isoform recovery was observed. The entrapment of the oc pDNA isoform occurred under non-binding conditions as well. The partial oc isoform elution from the column could be achieved by decreasing the flow rate of the elution mobile phase. The results suggested a reversible entrapment of the oc isoform in the restrictions within the pores of the monolithic material as well as within the intra-particle space of the non-porous particles. This phenomenon was observed on both types of the stationary phase morphologies and could only be connected to the size of a void space through which the pDNA needs to migrate. A prediction of reversible pDNA entrapment was successfully estimated with the calculation of Peclet numbers, Pe, which defines the ratio between a convective and diffusive mass transport.

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M. Limonta, N. Lendero Krajnc, U. Vidic, L. Zumalacárregui

Biochemical Engineering Journal 80 (2013) 14-18

The pIDKE2 plasmid is the main component of the CIGB's candidate vaccine against Hepatitis C virus (HVC), which is being used in HCV chronically-infected individuals during clinical trials phase 1 and 2. The designed downstream process of pIDKE2 plasmid produces up to 179 g/year. In order to conduct further improvements, modelling of the downstream process was performed. A methodology based on process analysis tools, such as experimental design and modelling was established to identify factors with the highest influence on production cost and the amount of annual plasmid. Taking into account that the pIDKE2 downstream process designed is in its initial stages of development, CIM technology was evaluated as a new manufacturing process on lab scale. Purity and recovery of CIM technology was better than porous particle matrix, thus SuperPro Designer was used in order to simulate the purification process. Cost efficiency optimization of the pIDKE2 downstream process was done with the simulation model.

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E. Maksimova, E. Vlakh, E. Sinitsyna, T. Tennikova
J. Sep. Sci. 2013, 36, 3741–3749

Ultrashort monolithic columns (disks) were thoroughly studied as efficient stationary phases for precipitation–dissolution chromatography of synthetic polymers. Gradient elution mode was applied in all chromatographic runs. The mixtures of different flexible chain homopolymers, such as polystyrenes, poly(methyl methacrylates), and poly(tert-butylmethacrylates) were separated according to their molecular weights on both commercial poly(styrene-co divinylbenzene).
disks (12 id × 3 mm and 5 × 5 mm) and lab-made monolithic columns (4.6 id × 50 mm) filled with supports of different hydrophobicity. The experimental conditions were optimized to reach fast and highly efficient separation. It was observed that, similar to the separation of monoliths of other classes of (macro)molecules (proteins, DNA, oligonucleotides), the length of column did not affect the peak resolution.
A comparison of the retention properties of the poly(styrene-co-divinylbenzene) diskshaped monoliths with those based on poly(lauryl methacrylate-co-ethylene dimethacrylate), poly(butyl methacrylate-co-ethylene dimethacrylate), and poly(glycidyl methacrylate-co-ethylene dimethacrylate) supports demonstrated the obvious effect of surface chemistry on the resolution factor. Additionally, the results of the discussed chromatographic mode on the fast determination of the molecular weights of homopolymers used in this study were compared to those established by SEC on columns packed with sorbent beads of a similar nature to the monoliths.

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Roy N D‘Souza, Ana M Azevedo, M Raquel Aires-Barros, Nika Lendero Krajnc, Petra Kramberger, Maria Laura Carbajal, Mariano Grasselli, Roland Meyer & Marcelo Fernández-Lahore

Vol. 1, No. 5, Pharmaceutical Bioprocessing (2013)

Downstream processing is currently the major bottleneck for bioproduct generation. In contrast to the advances in fermentation processes, the tools used for downstream processes have struggled to keep pace in the last 20 years. Purification bottlenecks are quite serious, as these processes can account for up to 80% of the total production cost. Coupled with the emergence of new classes of bioproducts, for example, virus-like particles or plasmidic DNA, this has created a great need for superior alternatives. In this review, improved downstream technologies, including aqueous two-phase systems, expanded bed adsorption chromatography, convective flow systems, and fibre-based adsorbent systems, have been discussed. These adaptive methods are more suited to the burgeoning downstream processing needs of the future, enabling the cost-efficient production of new classes biomaterials with a high degree of purity, and thereby hold the promise to become indispensable tools in the pharmaceutical and food industries.

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A. Ghanem, R. Healey, F. G. Adly

Analytica Chimica Acta 760 (2013) 1-15

Plasmid DNA (pDNA)-based vaccines offer more rapid avenues for development and production if compared to those of conventional virus-based vaccines. They do not rely on time- or labour-intensive cell culture processes and allow greater flexibility in shipping and storage. Stimulating antibodies and cellmediated components of the immune system are considered as some of the major advantages associated with the use of pDNA vaccines. This review summarizes the current trends in the purification of pDNA vaccines for practical and analytical applications. Special attention is paid to chromatographic techniques aimed at reducing the steps of final purification, post primary isolation and intermediate recovery, in order to reduce the number of steps necessary to reach a purified end product from the crude plasmid.

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